Heterocyclic amines (HCAs) are known mutagens and animal carcinogens formed in cooked meat and fish. Japanese people generally consume more fish than animal meat, and chopped and stir-fried method of meat preparation is favored as much as the grilled cooking method. Therefore, it is supposed that the foods contributing to HCA intake in Japan are different from those in western countries. However, dietary HCA intake levels and their main sources have not been estimated in Japan. The purpose of this study was to assess individual intake levels of specific HCAs in subjects of the Japan Public Health Center (JPHC)-based prospective study on cancer and cardiovascular disease (JPHC study). Individual intake levels of six predominant HCAs (Trp-P-1, MeIQ, MeIQx, 7,8-DiMeIQx, 4,8-DiMeIQx, and PhIP) were calculated for 39035 JPHC study participants (18290 men and 20745 women) from four geographic areas (9412 from Iwate, 12018 from Akita, 9896 from Nagano, and 7709 from Okinawa) based on a self-reported food frequency questionnaire (FFQ). Mean daily HCA intake levels (ng/kg per day) for subjects in the mainland areas (Iwate, Akita, and Nagano) were 1.06 (inter quartile range 0.50-1.35) in men and 1.10 (inter quartile range 0.53-1.40) in women. Mean daily HCA intake levels (ng/kg per day) for subjects in Okinawa Island were lower than those in the mainland; 0.83 (inter quartile range 0.33-1.04) in men and 0.92 (inter quartile range 0.33-1.18) in women. PhIP accounted for more than 60% of total HCA intake, followed by MeIQx and MeIQ. More than 50% of total HCA intake was derived from fish in the mainland, whereas more than 50% was from pork in Okinawa. Our study suggests that grilled fish are the major dietary sources of HCAs in Japanese, except those in Okinawa Island.